Thank you for your post, and I apologize for the late reply.
What fonts are being used on the layout? Is this happening with only one file? That is, if you create a new database file, use Arial font and print, does it work correctly? If you then change to the desired font, does it print correctly?
If you enter preview mode, do you see the correct fonts?
This may help rule out possible cross platform differences in how fonts are displayed.
I couldn't find a permanent way to resolve this quickly on all templates, but after tinkering with it, I found that once we changed the fonts and saved the changes, then it would print out with the correct font. It's going to be tedious part on the end users who deal with FileMaker Pro as they have to adjust the font on every single template they use (even if they change it to something else and then change it back to the correct one), but at least it will print out correctly now.
I'm not sure what might have changed that prevented all of the templates to print out with a generic font, but at least they have a work around now.
Perhaps the specified font wan't part of the list of fonts on the windows machines? There's an add/configure fonts option in the font menu when you are in layout mode that you might experiment with to see if adding a font or two resolves the issue without having to update each and every layout.